chr2-218414374-A-G

Variant names:

• chr2-218414374-A-G
• rs7607369

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.468 in 152,132 control chromosomes in the GnomAD database, including 19,409 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.47 (19409 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 41 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71269 AN: 152012 Hom.: 19406 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.744

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.522

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.468 AC: 71269 AN: 152132 Hom.: 19409 Cov.: 33 AF XY: 0.476 AC XY: 35369 AN XY: 74366

African (AFR) AF: 0.172 AC: 7156 AN: 41532

American (AMR) AF: 0.554 AC: 8449 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2105 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3851 AN: 5186

South Asian (SAS) AF: 0.651 AC: 3142 AN: 4826

European-Finnish (FIN) AF: 0.575 AC: 6068 AN: 10554

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38753 AN: 67990

Other (OTH) AF: 0.522 AC: 1101 AN: 2110

Alfa AF: 0.533 Hom.: 45645

Bravo AF: 0.451

Asia WGS AF: 0.663 AC: 2301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.32
PhyloP100		-0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7607369; hg19: chr2-219279097;